PXD056977

PXD056977 is an original dataset announced via ProteomeXchange.

Title	Perturbing RNA-mediated condensation of TFE3 oncofusion proteins to suppress renal cell carcinoma growth
Description	Chromosomal rearrangement-mediated oncofusion proteins are major oncogenic drivers, with high prevalence in pediatric cancers, which often have a poor prognosis. Liquid-like condensate formation has been reported in many oncofusion proteins, supporting their oncogenic signaling and transcriptional regulation. In this study, we report that RNA-mediated nuclear condensate formation plays an essential role in supporting the oncogenic transcription of TFE3 oncofusion proteins in MiT family translocation renal cell carcinoma (tRCC), which often occurs in children and adolescents and is considered an orphan disease in RCC lacking effective treatment. The RNA binding features in the fusion partners of transcription factor E3 (TFE3) support the nuclear condensate formation of TFE3 oncofusion proteins on the chromatin, thereby enabling RNA polymerase II (RNAPII) and other RNA binding proteins, e.g., paraspeckle component 1 (PSPC1), to co-condensate and form a transcriptional hub to support oncogenic transcription in tRCC. Perturbing TFE3 oncofusion condensate formation using a nanobody fused with maltose-binding protein (MBP) approach significantly suppresses tRCC cell growth in vitro and in vivo. In summary, our data highlight the pivotal role of RNA and RNA binding proteins in supporting the liquid-like condensate formation of oncofusion proteins and in promoting oncogenic transcription.
HostingRepository	PRIDE
AnnounceDate	2025-09-05
AnnouncementXML	Submission_2025-09-04_17:55:21.836.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Rongjie Zhao
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	biotinylated residue
Instrument	LTQ Orbitrap Elite

Revision	Datetime	Status	ChangeLog Entry
0	2024-10-20 03:19:28	ID requested
⏵ 1	2025-09-04 17:55:22	announced

10.1038/S41467-025-63761-Z;

submitter keyword: renal cell carcinoma, LC-MS/MS

Yun Nancy Huang
contact affiliation	Department of Translational Medical Sciences, School of Medicine, Texas A&M University, Houston, TX, USA
contact email	yun.huang@tamu.edu
lab head
Rongjie Zhao
contact affiliation	TEXAS A&M university
contact email	rogerzhao@zju.edu.cn
dataset submitter

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2025/09/PXD056977

PRIDE project URI

• PRIDE
  1. PXD056977
     1. Label: PRIDE project
     2. Name: Perturbing RNA-mediated condensation of TFE3 oncofusion proteins to suppress renal cell carcinoma growth